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Deep learning enables automated scoring of liver fibrosis stages.

ABSTRACT: Current liver fibrosis scoring by computer-assisted image analytics is not fully automated as it requires manual preprocessing (segmentation and feature extraction) typically based on domain knowledge in liver pathology. Deep learning-based algorithms can potentially classify these images without the need for preprocessing through learning from a large dataset of images. We investigated the performance of classification models built using a deep learning-based algorithm pre-trained using multiple sources of images to score liver fibrosis and compared them against conventional non-deep learning-based algorithms - artificial neural networks (ANN), multinomial logistic regression (MLR), support vector machines (SVM) and random forests (RF). Automated feature classification and fibrosis scoring were achieved by using a transfer learning-based deep learning network, AlexNet-Convolutional Neural Networks (CNN), with balanced area under receiver operating characteristic (AUROC) values of up to 0.85-0.95 versus ANN (AUROC of up to 0.87-1.00), MLR (AUROC of up to 0.73-1.00), SVM (AUROC of up to 0.69-0.99) and RF (AUROC of up to 0.94-0.99). Results indicate that a deep learning-based algorithm with transfer learning enables the construction of a fully automated and accurate prediction model for scoring liver fibrosis stages that is comparable to other conventional non-deep learning-based algorithms that are not fully automated.

SUBMITTER: Yu Y

PROVIDER: S-EPMC6207665 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Deep learning enables automated scoring of liver fibrosis stages.

Yu Yang Y Wang Jiahao J Ng Chan Way CW Ma Yukun Y Mo Shupei S Fong Eliza Li Shan ELS Xing Jiangwa J Song Ziwei Z Xie Yufei Y Si Ke K Wee Aileen A Welsch Roy E RE So Peter T C PTC Yu Hanry H

Scientific reports 20181030 1

Current liver fibrosis scoring by computer-assisted image analytics is not fully automated as it requires manual preprocessing (segmentation and feature extraction) typically based on domain knowledge in liver pathology. Deep learning-based algorithms can potentially classify these images without the need for preprocessing through learning from a large dataset of images. We investigated the performance of classification models built using a deep learning-based algorithm pre-trained using multipl ...[more]

PMID: 30375454

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Project description:IntroductionWe aim to apply deep learning to achieve fully automated detection and classification of the Cervical Vertebrae Maturation (CVM) stages. We propose an innovative custom-designed deep Convolutional Neural Network (CNN) with a built-in set of novel directional filters that highlight the edges of the Cervical Vertebrae in X-ray images.MethodsA total of 1018 Cephalometric radiographs were labeled and classified according to the Cervical Vertebrae Maturation (CVM) stages. The images were cropped to extract the cervical vertebrae using an Aggregate Channel Features (ACF) object detector. The resulting images were used to train four different Deep Learning (DL) models: our proposed CNN, MobileNetV2, ResNet101, and Xception, together with a set of tunable directional edge enhancers. When using MobileNetV2, ResNet101 and Xception, data augmentation is adopted to allow adequate network complexity while avoiding overfitting. The performance of our CNN model was compared with that of MobileNetV2, ResNet101 and Xception with and without the use of directional filters. For validation and performance assessment, k-fold cross-validation, ROC curves, and p-values were used.ResultsThe proposed innovative model that uses a CNN preceded with a layer of tunable directional filters achieved a validation accuracy of 84.63%84.63% in CVM stage classification into five classes, exceeding the accuracy achieved with the other DL models investigated. MobileNetV2, ResNet101 and Xception used with directional filters attained accuracies of 78.54%, 74.10%, and 80.86%, respectively. The custom-designed CNN method also achieves 75.11% in six-class CVM stage classification. The effectiveness of the directional filters is reflected in the improved performance attained in the results. If the custom-designed CNN is used without the directional filters, the test accuracy decreases to 80.75%. In the Xception model without the directional filters, the testing accuracy drops slightly to 79.42% in the five-class CVM stage classification.ConclusionThe proposed model of a custom-designed CNN together with the tunable Directional Filters (CNNDF) is observed to provide higher accuracy than the commonly used pre-trained network models that we investigated in the fully automated determination of the CVM stages.

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Deep learning enables automated scoring of liver fibrosis stages.

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Deep learning enables automated scoring of liver fibrosis stages.

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